Welcome to the SCOPe website!

SCOPe is a database developed
at the Berkeley Lab and UC Berkeley that extends
SCOP (version 1).
SCOPe classifies many structures
released since SCOP 1.75
through a combination of automation and manual curation,
and corrects some errors, aiming to have the
same accuracy as the fully hand-curated
SCOP releases.
SCOPe also
incorporates and updates the Astral database.

In addition to new SCOPe
releases, the SCOPe
website provides integrated access to data found in all
releases of the
SCOP and
Astral databases that feature
stable identifiers (i.e., those since release 1.55).
A history of all changes between
consecutive releases of SCOP and
SCOPe is available under the
Stats & History menu.

In order to facilitate use of SCOPe
data by SCOP and
Astral users, we provide
SCOPe data in parseable files in the same
formats as the SCOP and
Astral databases.
SCOPe uses the same stable identifiers
(e.g., sunid, sid, sccs) as were used for prior releases of
SCOP and
Astral.

Funding Alert: SCOPe support from the NIH ended in April 2016. John-Marc Chandonia is the primary maintainer and has continued to develop SCOPe using vacation time. Four proposals to the NIH for continued funding have been unsuccessful. Although Dr. Chandonia has obtained sufficient funding on other projects to remain employed for another year, SCOPe may shut down permanently in Summer 2019 as Dr. Chandonia will need to seek a new position.

Synopsis and News

Nearly all proteins have structural similarities with other proteins
and, in some of these cases, share a common evolutionary origin. The
SCOP database, created by manual
inspection and abetted by a battery of automated methods, aims to
provide a detailed and comprehensive description of the structural
and evolutionary relationships between all proteins whose structure
is known. As such, it provides a broad survey of all known protein
folds, detailed information about the close relatives of any
particular protein, and a framework for future research and
classification.

The Astral compendium provides databases
and tools useful for analyzing protein structures and their
sequences. It is partially derived from, and augments
SCOP(e).
Most of the resources provided here depend upon the
coordinate files maintained and distributed by the
Protein Data Bank.

In this release, we have developed new methodology to automate
the classification of new structures; this enabled us to automatically
classify some multi-chain domains
that could be confidently matched to existing, manually curated
SCOP
domains in the first 7 SCOP
classes. We are continuing to benchmark
our automated classification methods against prior versions of
SCOP,
to be sure the results of automation are completely
consistent with manual curation. In addition, we corrected several
more SCOP
bugs in this release—click on the
Stats & History
menu for details.

We've also added a number of additional mappings between
SCOP clades and Pfam families; thanks to Gabrielle Ho for providing
these.

Other improvements in SCOPe include an updated web
interface (which is still being developed and improved), and a
SQL back end (click the
Downloads
menu to obtain a copy).

SCOPe 2.03 was previously released
to the public as SCOP 1.75C. No
data have been harmed (or changed) in renaming the database.

License

All data in SCOPe (including the
data from older releases of SCOP
and Astral) are freely available to all users.

Pronunciation

There are several alternative pronunciations of the
vowels in the word SCOPe. All are
considered correct.

Funding

This work was supported by the National Institutes of Health
(R01-GM073109) through the U.S. Department of Energy under Contract
No. DE-AC02-05CH11231.